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I note that despite there being 52 reads passing filters for the reference genotype, the reference genotype quality is still only 1. Is RGQ affected by the presence of reads indicating a possible variant (4 in this case)? So the low RGQ score in this case reflects uncertainty over whether this position really is reference call (T/T), or if it might be a variant (A/A or A/T or T/A).

If I was being super strict about only including highly certain positions in my analysis would you recommend that I assign this position a missing genotype because I can't really be sure what it is?

Best Answer

Yes, this looks like a messy region. Notice the PL fields in the GVCF. Although the hom-ref genotype wins, the het genotype has a PL of 1. This means there really is not much confidence in the genotype. Basically, the genotype could either be hom-ref or het. Usually when the GQ is 0, we assign a ./. (no-call). However, since there is some slight evidence in this case for the hom-ref genotype, we assign the hom-ref genotype.

Yes, this looks like a messy region. Notice the PL fields in the GVCF. Although the hom-ref genotype wins, the het genotype has a PL of 1. This means there really is not much confidence in the genotype. Basically, the genotype could either be hom-ref or het. Usually when the GQ is 0, we assign a ./. (no-call). However, since there is some slight evidence in this case for the hom-ref genotype, we assign the hom-ref genotype.